Align kynurenine-oxoglutarate transaminase (EC 2.6.1.7) (characterized)
to candidate Ga0059261_1558 Ga0059261_1558 Aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::Q16773 (422 letters) >FitnessBrowser__Korea:Ga0059261_1558 Length = 389 Score = 197 bits (501), Expect = 5e-55 Identities = 126/385 (32%), Positives = 190/385 (49%), Gaps = 34/385 (8%) Query: 31 VNLGQGFPDFPPPDFAVEAFQHAVSGDFMLNQYTKTFGYPPLTKILASFFGELLGQEIDP 90 +NLGQGFPD + A A++ NQY G P L + +A+ + ++ P Sbjct: 30 INLGQGFPDGEGCVPVIRAAADALTT--RSNQYPPMAGLPALRQAIATHYTRHQQLDLSP 87 Query: 91 LRNVLVTVGGYGALFTAFQALVDEGDEVIIIEPFFDCYEPMTMMAGGRPVFVSLKPGPIQ 150 V+VT G A+ +F AL+ GDEVI+I+P +D Y P+ AGG L+PG Sbjct: 88 -EEVIVTSGATEAIAASFTALIAPGDEVILIQPLYDAYLPLVQRAGGVARLARLEPG--- 143 Query: 151 NGELGSSSNWQLDPMELAGKFTSRTKALVLNTPNNPLGKVFSREELELVASLCQQHDVVC 210 +W+L P L RT+ +V+N P NP G S EL +A+ C + D++ Sbjct: 144 --------SWRLTPAALEAAAGPRTRLIVVNNPVNPAGAKLSHGELADLAAFCVERDLIA 195 Query: 211 ITDEVYQWMVYDGHQHISIASLPGMWERTLTIGSAGKTFSATGWKVGWVLGPDHIMKHLR 270 I DEV++ +VYD +HI + ++PGM +RT+ IGSAGK F+ TGWKVGW+ + L Sbjct: 196 ICDEVWEHVVYDSARHIPLIAMPGMRDRTVKIGSAGKIFALTGWKVGWMCAAAPLAAVLA 255 Query: 271 TVHQNSVFHCPTQSQAAVAESFEREQLLFRQPSSYFVQFPQAMQRCRDHMIRSLQSVGLK 330 HQ F Q AVAE E + ++ QR RD + L + G + Sbjct: 256 RAHQFLTFSTAPNLQWAVAEGLETQ-------DAWIADSIVGFQRSRDRLAAGLTAAGYR 308 Query: 331 PIIPQGSYFLITDISDFKRKMPDLPGAVDEPYDRRFVKWMIKNKGLVAIPVSIFYSVPHQ 390 ++P G+ + ++ DL + +D F +++ G+ AIPVS FY+ + Sbjct: 309 -VLPSGATWFLS---------IDLAASGIALHDAAFCDRLVEEIGVAAIPVSAFYA---E 355 Query: 391 KHFDHYIRFCFVKDEATLQAMDEKL 415 H R CF K +A L E++ Sbjct: 356 APVTHLARLCFAKADAVLDTAIERM 380 Lambda K H 0.323 0.139 0.435 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 380 Number of extensions: 14 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 422 Length of database: 389 Length adjustment: 31 Effective length of query: 391 Effective length of database: 358 Effective search space: 139978 Effective search space used: 139978 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory